Publications
Detailed Information
The Development and Applications of Models for Molecular Problems : 분자 수준의 문제를 풀기 위한 모델의 개발 및 적용
| DC Field | Value | Language |
|---|---|---|
| dc.contributor.advisor | 신석민 | - |
| dc.contributor.author | 김태래 | - |
| dc.date.accessioned | 2017-07-14T05:51:34Z | - |
| dc.date.available | 2017-07-14T05:51:34Z | - |
| dc.date.issued | 2013-02 | - |
| dc.identifier.other | 000000008175 | - |
| dc.identifier.uri | https://hdl.handle.net/10371/125228 | - |
| dc.description | 학위논문 (박사)-- 서울대학교 대학원 : 화학부, 2013. 2. 신석민. | - |
| dc.description.abstract | We have proposed revisions for a pre-existing homology-based protein structure modeling tool interfaced with the CHARMM program in order to solve its derivative discontinuity problem, to suggest a simplified form of restraining functions, and to optimize several parameters. We have also developed new statistical potential energy functions for various protein torsion angle combinations. The utilities of the modeling tools and the statistical functions are examined for a large number of protein targets used in critical assessment of protein structure prediction (CASP). For excited state problems, multireference quantum chemical treatment, based on complete active space self-consistent field (CASSCF) method, has been applied to several model systems. | - |
| dc.description.tableofcontents | List of Figures v
List of Tables xxi Abstract xxix 1 Overview 1 I Development and Application of Homology Modeling strategy 3 2 The Need for Model Protein Structures 5 3 Homology Modeling Module Development 13 3.1 Basic Settings 18 3.2 Derivative Discontinuity Problem 27 3.3 Miscellaneous Algorithms 30 3.4 Optimization of Core Parameters 35 3.4.1 Validation of Basic Settings 36 3.4.2 Preliminary Calculations 37 3.4.3 Hessian Optimization 48 3.4.4 Test Outside the Optimization Set 56 3.4.5 Starting Structure 62 4 Statistical Torsion Angle Potential 81 4.1 Construction 82 4.2 Illustration 85 4.3 Validation 92 4.3.1 Derivative Discontinuity 92 4.3.2 Barrier Passing 93 4.3.3 Crystal Packing Effect 96 4.3.4 Biased Source 103 4.3.5 The Effect of Redundant Sequences 103 4.3.6 Making Correction Terms 106 4.4 Secondary Structure Information 106 4.5 Application on Side Chain Conformations 108 5 Miscellaneous Applications 119 5.1 Illustrative Benchmark 119 5.2 A Hybrid Approach using NOE Data 129 II Applications of CASSCF Approximation 149 6 A Brief Review of CASSCF Method 151 7 Application of CASSCF Method 157 7.1 Active Space Problem 157 7.1.1 Fused Aromatic Ring System 158 7.1.2 O2{CO2 Anion Cluster 161 7.1.3 Dihalobenzene Anion 166 7.2 Case Study: Oxidation of Si(100) Surface 170 III Appendix 183 A Supplements for Algorithms 185 A.1 Cubic Spline 185 A.2 Quaternion 188 A.3 Gaussian Weight 190 A.4 Side Chain Torsion Angles 192 B Basic Quantum Chemistry 195 B.1 Schrödinger Equation 195 B.2 Born-Oppenheimer Approximation 197 B.3 Hartree-Fock Approximation 200 B.3.1 Hartree Product 200 B.3.2 Slater Determinant 201 B.3.3 Hartree-Fock Approximation 202 B.3.4 A Note on Basis set 203 B.4 Beyond Hartree{Fock: Electron Correlation 205 C Assessment Scores 209 D List of Proteins in Test Sets 213 D.1 55 CASP7 Test Sets 213 D.2 106 CASP9 Test Sets 214 D.3 400 NMR Targets 215 E Used programs 219 F Full code 221 F.1 The Script for Protein-like Scores 221 G Sample Inputs 225 G.1 CHARMM Modeling Input 225 G.2 CASSCF Calculation from Hartree-Fock 232 G.3 Spin-Orbit Coupling Evaluation 234 H List of Acronyms 237 국문초록 243 Bibliography 245 | - |
| dc.format | application/pdf | - |
| dc.format.extent | 7015455 bytes | - |
| dc.format.medium | application/pdf | - |
| dc.language.iso | en | - |
| dc.publisher | 서울대학교 대학원 | - |
| dc.subject | Homology modeling | - |
| dc.subject | Statistical potential | - |
| dc.subject | Torsion angle | - |
| dc.subject | CASSCF | - |
| dc.subject | Excited state | - |
| dc.subject.ddc | 540 | - |
| dc.title | The Development and Applications of Models for Molecular Problems | - |
| dc.title.alternative | 분자 수준의 문제를 풀기 위한 모델의 개발 및 적용 | - |
| dc.type | Thesis | - |
| dc.contributor.AlternativeAuthor | Tae-Rae Kim | - |
| dc.description.degree | Doctor | - |
| dc.citation.pages | xxx, 262 | - |
| dc.contributor.affiliation | 자연과학대학 화학부 | - |
| dc.date.awarded | 2013-02 | - |
- Appears in Collections:
- Files in This Item:
Item View & Download Count
Items in S-Space are protected by copyright, with all rights reserved, unless otherwise indicated.